I think you're talking about 4Runners, but I believe this applies to Tacomas and Tundras too;
All of the various trims are well thought out and are good models worth buying. Each trim is also available in standard and Premium. Premium gets the nicer interior, stereo and exterior lights and turn signal on the side mirrors. I personally love the faux leather seats.
SR5: The Base Model, but has the same engine and transmission as TRD-OffRoad and TRD-Pro (although SR5 has dial selector for 4WD, where Off Road and Pro have a traditional lever to operate the 4WD). I think this is a good choice for someone how isn't going to off road at all, or not too heavily- or for someone keen to build up their own monster of a beast.
TRD Off Road: (Previously known as the Trail): This supplies rear locker, traction control and optional KDSS. KDSS is hydraulically actuated sway bars that allows for flat cornering and better handling on the road- and increased flex off road. I've also been told KDSS can actually reach down a little bit if that wheel is off the ground. I have this and love it. The KDSS suspension can also be lifted up to 3 inches. While Crawl Control is an interesting feature of the traction control, its not something you're going to be using a lot. On the other hand, A-Trac acts like a front locker and you'll be happy to have it. I think the Off Road is good for people looking to do a decent amount of wheeling, but like keeping things relatively close to stock.
TRD-Pro: This is the High Profit model for the dealerships. With bad-ass styling and engaging special colors, these will sell for at least $50K- as opposed to $42k for a TRD-Off Road Premium. The Pro has a long travel suspension and sits about 2 in higher than the other models. The Pro has all the same traction goodies and rear locker as the Off Road (but no KDSS). I think the Pro is good for people who want to do a lot of off roading and want to look baller doing it. But I don't think this is a good choice for someone who wants to modify it a lot (i.e. Lawndart) because you'll be removing all the things that make a Pro unique from the other models.
Limited: This is the swanky full time AWD (with center locking diff) model and costs are probably close to the TRD-Pro. The Limited looks different from the front and has a much nicer interior than the others. It also sits on 20in wheels (the others have 17in). While the TRD Off-Road has optional KDSS to improve handling, the Limited has an older system called XREAS. This system uses fluid filled lines running from front right to rear left and left front to right rear shock absorbers. Unlike KDSS, XREAS can not be lifted. I think the Limited is good for those not off roading as much as driving on snowy roads- but I have seen pics of lifted Limiteds on big wheels (I don't know exactly how they do it).